Current and Future Molecular Testing in NSCLC, What Can We Expect from New Sequencing Technologies?

Garinet, Simon; Laurent‐Puig, Pierre; Blons, Hélène; Oudart, Jean Baptiste

doi:10.3390/jcm7060144

Cited by 59 publications

(60 citation statements)

References 128 publications

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“…For example, the Therascreen EGFR PCR kit ® (Qiagen, Inc.) is a commercial quantitative (q)PCR kit and has been widely adopted for clinical practice; however, this method is time-consuming and possesses certain procedural complexities, for example, requiring several temperature changes during DNA amplification (11). Next-generation sequencing has improved the efficiency of oncogene testing by high-throughput sequencing, which can detect dozen of mutations at the same time, but the high-cost of this technique limits its clinical usage (13,14). Therefore, detecting oncogenic mutations using a simple, easy and highly reproducible method remains a challenge.…”

Section: Introductionmentioning

confidence: 99%

A novel loop‑mediated isothermal amplification method for efficient and robust detection of EGFR mutations

et al. 2020

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The activation of somatic mutations conferring sensitivity to epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors has been widely used in the development of advanced or metastatic primary lung cancer therapy. Therefore, identification of EGFR mutations is essential. In the present study, a loop-mediated isothermal amplification (LAMP) method was used to identify EGFR mutations, and its efficiency was compared with the Therascreen quantitative PCR assay. Using LAMP and Therascreen to analyze surgically resected tissue samples from patients with pulmonary adenocarcinoma, EGFR mutations were observed in 32/59 tumor samples (LAMP) and 33/59 tumor samples (Therascreen). Notably, the LAMP assay identified one tumor as wild-type, which had previously been identified as a deletion mutation in exon 19 via the Therascreen assay (Case X). However, the direct sequencing to confirm the EGFR status of the Case X adhered to the results of the LAMP assay. Further experiments using Case X DNA identified this exon 19 deletion mutation using both methods. In addition, a novel deletion mutation in exon 19 of the EGFR was identified. Overall, the present study shows that the LAMP method may serve as a valuable alternative for the identification oncogene mutations.

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Section: Introductionmentioning

confidence: 99%

A novel loop‑mediated isothermal amplification method for efficient and robust detection of EGFR mutations

et al. 2020

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“…Most of the reluctance to use cytology specimens for PD‐L1 testing arises from the belief that fixing the specimen in alcohol‐based fixatives rather than neutral buffered formalin (NBF), the standard fixative for histology specimens, might compromise the antigenicity of PD‐L1 and reduce its level of expression Alcohol‐based fixatives not only provide finer microscopic morphological detail but also cause less damage to RNA and DNA, and this is crucial for optimizing the results of next‐generation sequencing, a technique that is being increasingly applied to the routine profiling of NSCLC …”

Section: Introductionmentioning

confidence: 99%

Programmed death ligand 1 expression in EBUS aspirates of non–small cell lung cancer: Is interpretation affected by type of fixation?

Gosney

Haragan

Chadwick

et al. 2019

Cancer Cytopathology

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BACKGROUND:Much of the reluctance about using cytology specimens rather than histology specimens to assess programmed death ligand 1 (PD-L1) expression for guiding the use of immune modulating drugs in the management of non-small cell lung cancer (NSCLC) is based on the belief that the alcohol-based fixatives favored by cytopathologists might reduce the antigenicity of PD-L1 and lead to artifactually low expression levels and false-negative reporting. Therefore, this study was performed to determine whether there is any difference in PD-L1 expression between endobronchial ultrasound (EBUS)-guided aspirates of NSCLC fixed in alcohol-based fixatives and those fixed in neutral buffered formalin (NBF), the standard laboratory fixative for histology specimens. METHODS: The expression of PD-L1 was compared in 50 paired EBUS aspirates of NSCLC taken from the same lymph node during the same procedure. One aspirate of each pair was fixed in an alcohol-based fixative, and the other was fixed in NBF. RESULTS: In none of the 50 pairs was there any significant difference, qualitative or quantitative, in the strength, pattern, or extent of PD-L1 expression. In the great majority, the expression was identical, regardless of fixation. CONCLUSIONS: There is no evidence from this study showing that the use of alcohol-based fixatives has any effect on the expression of PD-L1 or its interpretation. Notwithstanding the general challenges in accurately assessing such expression in cytology specimens, pathologists should feel able to interpret them with confidence, and clinicians should feel able to rely on the results. Cancer Cytopathol 2020;128:100-106.

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“…9 The importance of CSF in guiding the treatment of cancerous brain lesions has been verified in some small-sample studies showing that it could relatively accurately represent the genomic mutation of brain tumors. [10][11][12][13][14] Nevertheless, data on brain metastases are still very limited. Therefore, the objective of the present study was to compare the results from CSF ctDNA with plasma ctDNA, plasma circulating tumor cells (CTCs), and brain tissue specimens in patients with brain metastasis from lung cancer.…”

Section: Introductionmentioning

confidence: 99%

Detection of circulating tumor DNA from non‐small cell lung cancer brain metastasis in cerebrospinal fluid samples

Yang

Xing

et al. 2020

Thoracic Cancer

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Background Evaluating the molecular characteristics of brain metastases is limited by difficult access and by the blood–brain barrier, which prevents circulating tumor DNA (ctDNA) from entering the blood. In this study, we aimed to compare the sequencing results from cerebrospinal fluid (CSF) ctDNA versus plasma ctDNA, plasma circulating tumor cells (CTCs), and brain tissue specimens from patients with brain metastasis from non‐small cell lung cancer (NSCLC). Methods This was a prospective study of 21 consecutive patients with NSCLC and brain metastasis diagnosed between April 2018 and January 2019. Samples of CSF and peripheral blood were obtained from all 21 patients. Brain tissues were obtained from five patients after surgical resection. Next‐generation sequencing was performed using the Ion system. Single nucleotide variants (SNVs) and small insertions or deletions (indels) were searched. Results Mutations were detected in the CSF ctDNA of 20 (95.2%) patients. The detection rate of epidermal growth factor receptor (EGFR) mutations in CSF ctDNA was 57.1% (12/21) whereas this rate was only 23.8% (5/21) in peripheral blood ctDNA and in CTCs. EGFR mutations were found in the CSF of 9 of 11 (81.8%) patients with leptomeningeal metastases, as compared with three of 10 (30%) patients with brain parenchymal metastases. Mutations were also detected in KIT, PIK3CA, TP53, SMAD4, ATM, SMARCB1, PTEN, FLT3, GNAS, STK11, MET, CTNNB1, APC, FBXW7, ERBB4, and KDR (all >10%). The status of EGFR and TP53 mutations was consistent between CSF ctDNA and brain lesion tissue in all five patients. Conclusion Sequencing of CSF ctDNA revealed specific mutation patterns in driver genes among patients with NSCLC and brain metastasis. Key points In some small‐sample studies, the importance of cerebrospinal fluid in guiding the treatment of cancerous brain lesions has been verified in that it may reflect genomic mutations of brain tumors relatively accurately. Cerebrospinal fluid is a new form of liquid biopsy that can be helpful in improving the management of patients with brain metastasis from non‐small cell lung cancer by detecting genetic abnormalities specific to brain metastases.

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Current and Future Molecular Testing in NSCLC, What Can We Expect from New Sequencing Technologies?

Cited by 59 publications

References 128 publications

A novel loop‑mediated isothermal amplification method for efficient and robust detection of EGFR mutations

A novel loop‑mediated isothermal amplification method for efficient and robust detection of EGFR mutations

Programmed death ligand 1 expression in EBUS aspirates of non–small cell lung cancer: Is interpretation affected by type of fixation?

Detection of circulating tumor DNA from non‐small cell lung cancer brain metastasis in cerebrospinal fluid samples

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